I seem to be missing something fundamental here.
For example
I have a number of door favourites. I use them to place doors in various situations but when I go back to the project a couple of weeks later I don't seem to be able to check which doors were placed using favourites and even which favourites where used to place the doors in the first place.
I don't seem to be able to manage the favourites.
What am I missing and how do I mange the application of favourites?

Favourites are more of a template to get you started, they are not linked to your model.

I suppose by combining Find & Select or a schedule and a clever naming scheme for your favourites you could set up something with a few steps that would allow for quickly changing things based on favourites, but really at that point it is just another way of changing settings.

Another approach would be to set up a schedule that looks for the door information that you want to check throughout the model. You could easily check for sizes, surfaces, door leaf types, fire rating - anything really. The pick them off in the schedule to update if they are not correct.